Tool to interactively create a Mouse Brain Atlas.
You need Matlab (tested on v. 2016) and SPM12.
Copy the files to a location of your choice. Make sure that you included your SPM12 path in Matlab. Open the application by 'ms_gui_mouseAtlas'
- On the left, there is a tree selection (starting with 'root'). From there you can explore the atlas.
- To 'select' a region right click its name in the tree selection. Selected regions are getting a bold green font.
- For a visual presentation you can click 'Update'. The axis on the right is updated. The color of a region of interest (ROI) is the same as indicated in the selection tree.
- Click 'Create Atlas'. After creation you can inspect the result (a figure opens automatically). In total, the app will create 4 files:
- the annotation atlas (matching the Allen avg template)
- a txt file linking the numbers with the names of regions
- the Allen atlas average template
- an annotation file in paxinos space (suffix '_inPax')
A manual can be found in the doc folder.
You can find an usage example in the example folder. This example extracts ROI time courses from a 4D nifty file and calculates a correlation matrix. The used atlas was created with this application. Make sure to unzip 'data.zip' before usage!
When you use this software, please cite: "Sack M, Zheng L, Gass N, Ende G, Sartorius A, Weber-Fahr W (2020) Interactive tool to create adjustable anatomical atlases for mouse brain imaging. MAGMA doi:10.1007/s10334-020-00866-0."